Spock let out an exhale that - with other people - would have indicated they were exasperated with themselves or a situation, and come out much more abruptly. But with him, it was slowly done, controlled. He set his coffee aside, reaching out with one hand to touch his fingertips against her arm, to try to still her for a few seconds and reason with her.
"This was not a mistake. Even if you are angry, I would have you know...I did not want to be a hindrance to you or leave you feeling obligated to wait for me, when there was the possibility that our lives would not converge again." He paused and whereas there was that little hitch in her voice, his own voice became more strained, even as it stayed low. As though he was keeping things bottled in, to not make things harder on either of them. "Do not make the mistake of thinking it didn't pain me to let you go. It did. You are irreplaceable, Nyota. I would like to see you again, if you are unable to forgive me for that profound...miscalculation."
He removed his hand, because he knew too well that further contact while Uhura was in a mood wasn't suggested. Brevity was best, until she had some time to think it over, just as he would.